I dunno about Tsukiji, Kamakura, shinkansen to Kyoto all on the same day. So where will your bags be during this day trip? You won't want to go back to Shinagawa to get them. I guess they could be stored in the lockers at Yokohama station if the bags aren't too large; there are coin lockers but they are a bit hard to find.

Also bear in mind that the ride between Kamakura and Yokohama is about an hour round trip, and then you still have to get to Shin-Yokohama to catch the shinkansen.

Finally, the main attractions in Kamakura are temples and a Buddha statue -- and guess what you will be seeing a zillion of in Kyoto! I think your time would be better spent getting to Kyoto earlier and doing a bit of sightseeing on your day of arrival there. Your time in Kyoto is quite short.

Last day in Hiroshima, take a day trip to Miyajima. Must see if you're in the area (and you will be in the area).

Incidentally, the walk between Shibuya and Harajuku et al is a bit longer than you might think. And the distance between Shinagawa and Shibuya is definitely longer than you might think. However, the Yamanote line is cheap, no more than Y150 between any of those points.

Shinagawa isn't really out of the way at all. No place in Tokyo close to a major station is out of the way, and Shinagawa is definitely a major station.